title: Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
abstract: Over the last 15 years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (K(d)>10(-6)M) complexes, which often fail to crystallize. This chapter emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semiautomated NMR assignment methods, and structure determination of protein-ligand complexes by NMR.
authors.affiliation: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Ziarek
authors.forename: Francis C
authors.initials: FC
authors.lastname: Peterson
authors.forename: Betsy L
authors.initials: BL
authors.lastname: Lytle
authors.forename: Brian F
authors.initials: BF
authors.lastname: Volkman
mesh_terms: D057205:Automation, Laboratory; D001665:Binding Sites; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D006860:Hydrogen Bonding; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins